Electrophoresis is commonly used to separate biological molecules, such as deoxyribonucleic acid (“DNA”), ribonucleic acid (“RNA”), proteins, etc., according to size or length.
DNA base sequencing and fragment analysis are among the most useful embodiments of electrophoresis separations. In DNA base sequencing, for example, a DNA sequencing product is denatured and the resulting single stranded DNA sample is applied to an electrophoresis gel for separation.
Unfortunately, it is not uncommon to encounter sequencing errors involving specific sequences which are difficult to resolve. One such problem, called a “compression,” occurs when the single-stranded fragments anneal to themselves to form a “hairpin” structure at a particular position. The following schematic generally illustrates such an occurrence:

This may cause the fragment to migrate more quickly through the gel than one would expect from its length, which can result in bands that run very close together, sometimes overlapping one another.